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Yorodumi- PDB-1gaf: 48G7 HYBRIDOMA LINE FAB COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gaf | ||||||
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Title | 48G7 HYBRIDOMA LINE FAB COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID | ||||||
Components | (CHIMERIC 48G7 FAB) x 2 | ||||||
Keywords | CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Potential therapeutics for SARS / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Wedemayer, G.J. / Patten, P.A. / Stevens, R.C. / Schultz, P.G. | ||||||
Citation | Journal: Science / Year: 1996 Title: The immunological evolution of catalysis. Authors: Patten, P.A. / Gray, N.S. / Yang, P.L. / Marks, C.B. / Wedemayer, G.J. / Boniface, J.J. / Stevens, R.C. / Schultz, P.G. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: A Genetic Approach to the Generation of Antibodies with Enhanced Catalytic Activities Authors: Lesley, S.A. / Patten, P.A. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gaf.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gaf.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gaf_validation.pdf.gz | 723.6 KB | Display | wwPDB validaton report |
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Full document | 1gaf_full_validation.pdf.gz | 729.7 KB | Display | |
Data in XML | 1gaf_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1gaf_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1gaf ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1gaf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23485.045 Da / Num. of mol.: 1 Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS Source method: isolated from a genetically manipulated source Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY ...Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY CHAIN CONSISTS OF THE VDJ VARIABLE DOMAIN FROM MOUSE AND THE C(H1) CONSTANT REGION FROM HUMAN Source: (gene. exp.) Homo sapiens (human) Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Production host: BL21 / References: GenBank: 4768677, UniProt: P01834*PLUS |
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#2: Antibody | Mass: 23209.020 Da / Num. of mol.: 1 Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS Source method: isolated from a genetically manipulated source Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY ...Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY CHAIN CONSISTS OF THE VDJ VARIABLE DOMAIN FROM MOUSE AND THE C(H1) CONSTANT REGION FROM HUMAN Source: (gene. exp.) Homo sapiens (human) Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Production host: BL21 / References: UniProt: P01857 |
#3: Chemical | ChemComp-NPE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 44.8 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 33282 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 |
Reflection | *PLUS Num. measured all: 121262 |
-Processing
Software |
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Refinement | Resolution: 1.95→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.3076 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |